On 31 December 2019, the World Health Organization (WHO) first learned of an outbreak of severe pneumonia of unknown etiology in Wuhan, Hubei Province, China (
1–
4), a city of ~11 million people. Of the initial 41 people hospitalized with unknown pneumonia by 2 January 2020, 27 (66%) had direct exposure to the Huanan Wholesale Seafood Market (hereafter, “Huanan market”) (
2,
5,
6). These first cases were confirmed to be infected with a novel coronavirus, subsequently named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and were suffering from a disease later named coronavirus disease 2019 (COVID-19). The initial diagnoses of COVID-19 were made in several hospitals independently between 18 and 29 December 2019 (
5). These early reports were free from ascertainment bias because they were based on signs and symptoms before the Huanan market was identified as a shared risk factor (
5). A subsequent systematic review of all cases reported to China’s National Notifiable Disease Reporting System by hospitals in Wuhan as part of the joint WHO-Chinese “WHO-convened global study of origins of SARS-CoV-2: China Part” (hereafter, “WHO mission report”) (
7) showed that 55 of 168 of the earliest known COVID-19 cases were associated with this market. However, the observation that the preponderance of early cases were linked to the Huanan market, alone, does not establish that the pandemic originated there.
Discussion
Several lines of evidence support the hypothesis that the Huanan market was the epicenter of the COVID-19 pandemic and that SARS-CoV-2 emerged from activities associated with the live wildlife trade there. Spatial analyses within the market show that SARS-CoV-2–positive environmental samples, including cages, carts, and freezers, were associated with activities concentrated in the southwest corner of the market. This is the same section where vendors were selling live mammals, including raccoon dogs, hog badgers, and red foxes, immediately before the COVID-19 pandemic. Multiple positive samples were taken from one stall known to have sold live mammals, and the water drain proximal to this stall, as well as other sewerages and a nearby wildlife stall on the southwest side of the market, tested positive for SARS-CoV-2 (
24). These findings suggest that infected animals were present at the Huanan market at the beginning of the COVID-19 pandemic; however, we do not have access to any live animal samples from relevant species. Additional information, including sequencing data and detailed sampling strategy, would be invaluable to test this hypothesis comprehensively.
In a related study, we inferred separate introductions of SARS-CoV-2 lineages A and B into humans from likely infected animals at the Huanan market (
38). We estimated the first COVID-19 case to have occurred in November 2019, with few human cases and hospitalizations occurring through mid-December (
38). A recent preprint (
24) confirms the authenticity of the CCDC report (data S1) and records additional positive environmental samples in the southwestern area of the market selling live animals. This report also documents the early presence of the A lineage of SARS-CoV-2 in a Huanan market environmental sample. This, along with the lineage A cases that we report in close geographical proximity to the market in December 2019, challenges the suggestion that the market was simply a superspreading event, which would be lineage specific. Rather, it adds to the evidence presented here that lineage A, like lineage B, may have originated at the Huanan market and then spread from this epicenter into the neighborhoods surrounding the market and beyond.
Several observations suggest that the geographic association of early COVID-19 cases with the Huanan market is unlikely to have been the result of ascertainment bias (see the supplementary text and tables S2 and S3) (
39). These include that (i) few, if any, cases among Huanan market–unlinked individuals are likely to have been detected by active searching in the neighborhoods around the market, only in hospitals, because all of the cases analyzed here were hospitalized (
7); (ii) public health officials simultaneously became aware of Huanan-linked cases both near and far from the Huanan market, not just the ones near it (fig. S11) (
5); (iii) Huanan market–unlinked cases would not be expected to live significantly closer to the market than linked cases if they had been ascertained as contacts traced from those market-linked cases; and (iv) seroprevalence in Wuhan was highest in the districts around the market (
40,
41). It is also noteworthy that the December 2019 COVID-19 cases that we consider here were identified based on reviews of clinical signs and symptoms, not epidemiological factors such as where they resided or links to the Huanan market (
7), and that excess deaths from pneumonia rose first in the districts surrounding the market (
42). Moreover, the spatial relationship with the Huanan market remains after removing the two-thirds of the unlinked cases residing nearest the market.
One of the key findings of our study is that “unlinked’ early COVID-19 patients, i.e., those who did not work at the market, did not know someone who did, and had not recently visited the market, resided significantly closer to the market than patients with a direct link to it. The observation that a substantial proportion of early cases had no known epidemiological link had previously been used as an argument against the Huanan market being the epicenter of the pandemic. However, this group of cases resided significantly closer to the market than those who worked there, indicating that they had been exposed to the virus at or near the Huanan market. For market workers, the exposure risk was their place of work, not their residential locations, which were significantly farther afield than those cases not formally linked to the market.
Our spatial analyses show how patterns of COVID-19 cases shifted between late 2019, when the outbreak began (
43), and early 2020, as the epidemic spread widely across Wuhan. COVID-19 cases in December 2019 were associated with the Huanan market in a manner unrelated to Wuhan population density or demographic patterns, unlike the wide spatial distribution of cases observed during later stages of the epidemic in January–February 2020. This observation fits with the evidence from other sources that SARS-CoV-2 was not widespread in Wuhan at the end of 2019. For example, no SARS-CoV-2–positive sera or influenza-like illness reports were recorded among more 40,000 blood donor samples collected up to December 2019 (
44,
45), and none of thousands of samples taken from patients with influenza-like illness at Wuhan hospitals in October to December 2019 tested for SARS-CoV-2 RNA was positive (
7).
The sustained presence of a potential source of virus transmission into the human population in late 2019, plausibly from infected live mammals sold at the Huanan market, offers an explanation of our findings and the origins of SARS-CoV-2. The pattern of COVID-19 cases reported for the Huanan market, with the earliest cases in the same part of the market as the wildlife sales and evidence of at least two introductions (
38), resembles the multiple cross-species transmissions of SARS-CoV-2 subsequently observed during the pandemic from animals to humans on mink farms (
46) and from infected hamsters to humans in the pet trade (
47). There was an extensive network of wildlife farms in western Hubei Province, with hundreds of thousands of wild mammals including civets, ferret badgers, and raccoon dogs on farms in Enshi Prefecture, which supplied the Huanan market (
48). This region of Hubei contains extensive cave complexes housing
Rhinolophus bats, which carry SARSr-CoVs (
49). SARS-CoV-1 was recovered from farmed masked palm civets (
Paguma larvata) from Hubei in 2003 and 2004 (
20). The animals on these farms (nearly 1 million) were rapidly released, sold, or killed in early 2020 (
48), apparently without testing for SARS-CoV-2 (
7). Live animals sold at the market (
Table 1) were apparently not sampled either. By contrast, during the SARS-CoV-1 outbreaks, farms and markets remained open for more than a year after the first human cases occurred, allowing sampling of viruses from infected animals (
20).
The live animal trade and live animal markets are a common theme in virus spillover events (
21–
23,
50), with markets such as the Huanan market selling live mammals being in the highest risk category (
51). The events leading up to the COVID-19 pandemic mirror the SARS-CoV-1 outbreaks from 2002 to 2004, which were traced to infected animals in the Guangdong, Jiangxi, Henan, Hunan, and Hubei provinces in China (
20). Maximum effort must now be applied to elucidate the upstream events that might have brought SARS-CoV-2 into the Huanan market, culminating in the COVID-19 pandemic. To reduce the risk of future pandemics, we must understand, and then limit, the routes and opportunities for virus spillover.
Acknowledgments
We thank the researchers who generated the geospatial and environmental sample data and the members of the China team involved in producing the WHO mission report for the maps that made this work possible; M. Standaert, B. LaFleur, @babarlelephant, M. Boni, F. Débarre, and B. Pierce for comments and assistance; WorldPop.org for making population density and demographic data from Wuhan freely available; the patients, clinicians, and researchers whose data made this research possible; and the five reviewers for insightful comments and feedback.
Funding: This project has been funded in part with federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Department of Health and Human Services (contract no. 75N93021C00015 to M.W.). J.I.L. acknowledges support from the NIH (grant 5T32AI007244-38). S.A.G. acknowledges support from the NIH (grant F32AI152341). J.E.P. acknowledges support from the NIH (grant T15LM011271). J.O.W. acknowledges support from NIH (grants AI135992 and AI136056). D.L.R. acknowledges support from the Medical Research Council (grant MC_UU_12014/12) and the Wellcome Trust (grant 220977/Z/20/Z). M.A.S., P.L., and A.R. acknowledge support from the Wellcome Trust (collaborators award 206298/Z/17/Z – ARTIC network), the European Research Council (grant no. 725422 – ReservoirDOCS), and the NIH (grant R01AI153044). A.L.R. is supported by the Canadian Institutes of Health Research as part of the Coronavirus Variants Rapid Response Network (CoVaRR-Net; CIHR FRN#175622) and acknowledges that VIDO receives operational funding from the Canada Foundation for Innovation – Major Science Initiatives Fund and from the Government of Saskatchewan through Innovation Saskatchewan and the Ministry of Agriculture. M.K. receives funding from the European Union’s Horizon 2020 research and innovation program (grant no. 874735, VEO, Versatile Emerging Infectious Disease Observatory). R.F.G. acknowledges support from the NIH (grants R01AI132223, R01AI132244, U19AI142790, U54CA260581, U54HG007480, and OT2HL158260), the Coalition for Epidemic Preparedness Innovation, the Wellcome Trust Foundation, Gilead Sciences, and the European and Developing Countries Clinical Trials Partnership Programme. E.C.H. is supported by an Australian Research Council Laureate Fellowship (FL170100022). K.G.A. acknowledges support from the NIH (grants U19AI135995, U01AI151812, and UL1TR002550).
Author contributions: Conceptualization: M.W., K.G.A.; Data curation: M.W., A.R., K.G.A.; Formal analysis: M.W., J.I.L., A.C.-C., L.M., J.E.P., M.U.G.K., M.A.S., A.L.R., D.L.R., S.A.G., A.R., J.O.W., R.F.G., P.L., E.C.H., K.G.A.; Funding acquisition: M.W., J.I.L., A.C.-C., L.M., J.E.P., M.U.G.K., M.A.S., A.L.R., D.L.R., S.A.G., A.R., J.O.W., R.F.G., P.L., E.C.H., K.G.A.; Investigation: M.W., J.I.L., A.C.-C., L.M., J.E.P., M.U.G.K., M.A.S., M.K., A.L.R., D.L.R., C.N., S.A.G., A.R., J.O.W., R.F.G., P.L., E.C.H., K.G.A.; Methodology: M.W., J.I.L., A.C.-C., L.M., J.E.P., M.U.G.K., M.A.S., A.L.R., D.L.R., S.A.G., A.R., J.O.W., R.F.G., P.L., E.C.H., K.G.A.; Project administration: M.W., K.G.A.; Resources: M.W., J.O.W., K.G.A.; Software: L.M., J.I.L., J.E.P., J.O.W., P.L., A.R.; Supervision: M.W., J.O.W., K.G.A.; Validation: M.W., L.M., J.I.L., J.E.P., P.L., J.O.W., K.G.A.; Visualization: M.W., J.I.L., L.M., J.E.P., A.L.R., A.R., J.O.W., R.F.G., P.L., E.C.H., K.G.A.; Writing – original draft preparation: M.W., R.F.G.; Writing – review and editing: M.W., J.I.L., A.C.-C., L.M., J.E.P., M.U.G.K., M.A.S., M.K., A.L.R., C.N., D.L.R., S.A.G., A.R., J.O.W., R.F.G., P.L., E.C.H., K.G.A.
Competing interests: J.O.W. receives funding from the Centers for Disease Control and Prevention (CDC) through contracts to his institution unrelated to this research. M.A.S. receives funding from Janssen Research & Development, the US Food & Drug Administration, and the US Department of Veterans Affairs through contracts and grants unrelated to this research. R.F.G. is a cofounder of Zalgen Labs, a biotechnology company developing countermeasures for emerging viruses. M.W., A.L.R., A.R., M.A.S., E.C.H., S.A.G., J.O.W., and K.G.A. have received consulting fees and/or provided compensated expert testimony on SARS-CoV-2 and the COVID-19 pandemic. M.K. has participated in the second WHO mission to China to study the origins of the pandemic and has served as scientific adviser on emerging disease preparedness to the Guangdong CDC before 2020.
Data and materials availability: Data and code for this manuscript are available from (
53). We acquired the Weibo dataset from (
26).
License information: This work is licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. To view a copy of this license, visit
https://creativecommons.org/licenses/by/4.0/. This license does not apply to figures/photos/artwork or other content included in the article that is credited to a third party; obtain authorization from the rights holder before using such material.
Duplicate, missing, and biased data in the Worobey et al. study undermine their main result
A claimed main result from the study of Worobey et al. [1] is that the 35 mapped COVID-19 cases with a documented epidemiological link to the Huanan Seafood Wholesale Market (the Huanan market) were significantly further away from the market location than the 120 cases which had no such link (“The cases with no known link to the market on average resided closer to the market than the cases with links to the market (p = 0.029)” and “[o]ne of the key findings of our study is that ‘unlinked’ early COVID-19 patients, i.e., those who did not work at the market, did not know someone who did, and had not recently visited the market, resided significantly closer to the market than patients with a direct link to it. The observation that a substantial proportion of early cases had no known epidemiological link had previously been used as an argument against the Huanan market being the epicenter of the pandemic. However, this group of cases resided significantly closer to the market than those who worked there, indicating that they had been exposed to the virus at or near the Huanan market.”)
The above result followed from the observed difference between the two corresponding samples of cases, with median distances to the Huanan market of 5.7 km and 4.0 km, respectively, which Worobey et al. report to be borderline statistically significant (p = 0.029 at α = 0.05 level; Wilcoxon rank sum test). However, as is directly shown below with their own data, this result is problematic for two reasons:
1. Their sample data file for the n=35 statistical background (“distance_popdensityagegroups_null_35.csv” retrieved from the study’s data collection at https://github.com/sars-cov-2-origins/huanan-market/tree/main/data) is a duplicate of the n=120 data file (“distance_popdensityagegroups_null_120.csv”), which also means that the n=35 sampling data itself is missing in their study. [Of note, this problem was already pointed out to Worobey et al. in a Technical Comment (manuscript ade3852 submitted to Science magazine on 12 August 2022; editorially rejected on 4 October 2022), but it has not been addressed in their first written reply (email letter attached to the 4 October 2022 editorial decision email) nor following their second written reply (email letter on the 17 November 2022).]
2. Worobey et al. did not conduct the necessary negative control, which specifically entails the rejection of the main hypothesis (i.e, the n=35 sample median distance to the Huanan market is greater than the n=120 sample median distance) on their chosen statistical background. Only if this negative control were passed their main claim would be specifically supported by their statistical data.
Given this data duplication in the Worobey et al. study, the Wilcoxon rank sum test for the n=35 and n=120 background samples trivially passes this negative control (due to the duplication, both samples are identical with zero shift) and therefore cannot be used to support their claim.
As the n=35 background distribution itself is missing in their study's data, the closest two background distributions available in their data set (in both directions of the sample size, n=36 and n=11) can be used instead for the negative control (files “distance_popdensityagegroups_null_36.csv” and “distance_popdensityagegroups_null_11.csv”). Yet this necessary negative control failed: the Wilcoxon rank sum test did reject the hypothesis that the median distances from n=36 and n=11 distributions were drawn without a positive shift when compared with the n=120 distances (p = 0.019 and p = 0.030, respectively). Thus the main result of Worobey et al. is directly undermined by their own statistical background, which for n=36 and n=11 produces biased median distances that are already significantly greater than the n=120 medians.
Therefore, in contradiction to the key claim by Worobey et al., it cannot be inferred that the observed closer proximity of the 120 cases not epidemiologically linked to the Huanan market is due to their origin being at that market. Together with a previous technical comment [2], which directly questioned the exclusive Huanan market origin of the earliest SARS-CoV-2 lineage B cases, this evidence further invalidates the market origin hypothesis of SARS-CoV-2.
To date (10 April 2023), Worobey et al. and Science editors have, after their official and documented acknowledgements of these duplicate and missing data problem on the 17th and on the 21st November 2022, respectively, failed (a) to address and to resolve said points 1 and 2 above as well as the previous point in the Science eLetter [2] from 16 October 2022, and (b) to correct the scientific record in question despite their own official announcements to do so.
References
[1] Worobey M, Levy JI, Malpica Serrano L, et al. The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic. Science. 2022;377(6609):951-959. doi:10.1126/science.abp8715
[2] Lisewski AM The geospatial data of Worobey et al. statistically links the Wuhan Institute of Virology with the Huanan Seafood Wholesale Market (16 October 2022 electronic eLetter response to Worobey et al. (2022) The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic Science, Vol 377, Issue 6609, pp. 951-959 URL:https://www.science.org/doi/10.1126/science.abp8715#elettersSection)
This article
Did the investigators have access to Covid testing data on staff working in labs in Wuhan during late 2019? If any positives (RT-PCR or seropositivity) were found, where did these individuals live and how does their spatial location compare to what is shown in this paper?
SARS-CoV-2 origin is still unknown
In their article, Worobey et al. [1] confirm that the Huanan market served as an early superspreading event for COVID-19, but provide no definitive evidence that SARS-CoV-2 was first transmitted to humans from wildlife sold there. Out of the 457 animals (18 species) tested from the market, all were negative [2].
Although Worobey et al. date the first potential market-associated case to November 2019, wastewater surveillance and retrospective analysis of human samples raise the possibility that the virus may have been spreading in France, Brazil and Italy in September-November 2019 [3]. Details about the first official human cases unconnected to the market are still unclear [4–6].
Worobey et al. examine SARS-CoV-2 positive environmental samples at the market, collected in January 2020 [2]. These samples are probably of human origin because the corresponding published sequences are identical to the ones found in patients [2]. Since the earliest detected cases at the market occupied stalls too dispersed for their direct contamination from 1-2 animal sources [7] and appear to be due to human-to-human transmissions outside of stalls, analysis of spatial distribution of positive samples is not relevant to infer the place of the first animal contamination. In fact, what the Worobey et al. density risk map may locate is the epicenter of a superspreading event, an area in the market’s southwest where public toilets and a closed Mahjong room are found.
The distribution of human positive cases at the market is consistent with both a zoonotic introduction that would have occurred several weeks before the first cases were detected, and an introduction of the virus to the market by an externally infected person.
Worobey et al. situate the epicenter of earliest cases to a district that also includes the Wuhan Center for Disease Control laboratory, which conducts field and laboratory research on bat viruses [8] and which moved into a new location only 500 meters from the market on 2 December 2019, something they do not mention. The authors do not consider the possibility that this laboratory could be the site of the initial human case, but acknowledge that “upstream events” and “exact circumstances” remain “obscure”.
Although it may be challenging to distinguish an accidental infection during laboratory or field work from one that occurred between an animal and a market vendor, retrospective analyses of 2019 human samples available inside and outside China could prove informative to uncover upstream events.
In summary, the Huanan market can be considered as the epicenter of an early superspreader event but it is not possible to conclude that it was the entry point of SARS-CoV-2 into the human population. It is not yet clear how exactly SARS-CoV-2 originated. All hypotheses need to be investigated, including the possibility of a lab accident, as recently summarized in the SAGO committee report [9] and in the Lancet commission report [10].
References
1. Worobey M, Levy JI, Serrano LM, et al. The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic. Science;0:abp8715. doi:10.1126/science.abp8715
2. Gao G, Liu W, Liu P, et al. Surveillance of SARS-CoV-2 in the environment and animal samples of the Huanan Seafood Market. In Review 2022. doi:10.21203/rs.3.rs-1370392/v1
3. Canuti M, Bianchi S, Kolbl O, et al. Waiting for the truth: is reluctance in accepting an early origin hypothesis for SARS-CoV-2 delaying our understanding of viral emergence? BMJ Glob Health 2022;7:e008386.
4. Huang C, Wang Y, Li X, et al. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. The Lancet 2020;395:497–506. doi:10.1016/S0140-6736(20)30183-5
5. Zhou P, Yang X-L, Wang X-G, et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 2020;579:270–3.
doi:10.1038/s41586-020-2012-7
6. Joint WHO-China Study Team. WHO-convened Global Study of Origins of SARS-CoV-2: China Part. World Health Organisation 2021. https://www.who.int/health-topics/coronavirus/origins-of-the-virus
7. Courtier-Orgogozo V, de Ribera FA. SARS-CoV-2 infection at the Huanan seafood market. Environ Res 2022;214:113702.
8. Guo W-P, Lin X-D, Wang W, et al. Phylogeny and origins of hantaviruses harbored by bats, insectivores, and rodents. PLoS Pathog 2013;9:e1003159.
9. Scientific Advisory Group for the Origins of Novel Pathogens (SAGO). Preliminary Report. 2022.https://www.who.int/publications/m/item/scientific-advisory-group-on-the-origins-of-novel-pathogens-report (accessed 22 Sep 2022).
10. Sachs JD, Karim SSA, Aknin L, et al. The Lancet Commission on lessons for the future from the COVID-19 pandemic. The Lancet 2022;0. doi:10.1016/S0140-6736(22)01585-9.
Note: The views expressed here are those of the authors and not necessarily those of their respective institutions.
VCO and FG received funding from the "Who I am?" Labex to elucidate the proximal origins of the SARS-CoV-2 virus.
CDB has received a writer's fee from the United Nations Environment Programme for the forthcoming report "Covid-19: a warning".
RHE has received consulting fees on SARS-CoV-2 and the COVID-19 pandemic and receives funding from the National Institutes of Health and Janssen under grants and contracts unrelated to SARS-CoV-2 and the COVID-19 pandemic.
NP receives funding from the National Institutes of Health for vaccine research including COVID-19.
Competing interests for RAB, JMC, ED, JPD, HK, BK, ML, SM, MR, GT, NP: None declared.
Selective and cross-reactive SARS-CoV-2 T-cell epitopes in unexposed humans
The eLetter of Edward Parr cites the failure to include the study by Basaveraju et al. in this assessment. Basaveraju et al. did not include an appropriate control in their study; for example, analysis of the same number of samples from the same blood banks taken prior to the likely first identification of SARS-Cov-2 in Western countries, assuming availability. There are multiple papers describing the presence of cross-reactive antibodies in individuals who had (nominally) never been exposed to SARS-Cov-2; for example: Mateus et al., Selective and cross-reactive SARS-CoV-2 T-cell epitopes in unexposed humans, SCIENCE 4 Aug 2020 Vol 370, Issue 6512, pp. 89-94, DOI: 10.1126/science.abd3871. The source of these cross-reactive antibodies is proposed to be through exposure to the human coronaviruses associated with the "common cold". Unfortunately, the politicization of responsibility for the pandemic has precluded access to all the relevant data available in China to determine the most likely source and transmission routes of SARS-Cov-2. Based on the data presented in this paper, the Huanan market would appear to be a likely epicentre for the initial transmission of the virus in Wuhan.
The geospatial data of Worobey et al. statistically links the Wuhan Institute of Virology with the Huanan Seafood Wholesale Market
Worobey et al. [1] present a geometrical distance analysis of early COVID-19 cases within the city of Wuhan between December 2019 and January 2020. The results of this analysis lead them to conclude that during the earliest stages of the outbreak SARS-CoV-2 “lineage A, like lineage B, may have originated at the Seafood Wholesale Market then spread from this epicenter into the neighborhoods surrounding the market and then beyond”. This conclusion was already assumed to be valid in a companion study [2] about these two suggested root SARS-CoV-2 lineages in humans. A key methodological input in [1] was the choice of the median as the geometrical distance measure from the reference location of the Huanan Seafood Wholesale Market (abbreviated here as Huanan market). These medians were calculated from samples of mapped COVID-19 cases and from expected random null locations in Wuhan sampled from the city’s overall population density and matched for age. However, with respect to its possible statistical effects and epidemiological implications, the selective use of “medians rather than means” ([1], Supplementary Materials) was not sufficiently justified by the authors, as they simply discarded the difference between means and medians altogether as “outliers”.
In the context of COVID-19 outbreak epidemiology and the origin question, medians of geometrical distances are a questionable measure because any geometrical change (e.g., clustering) in the upper half of the sampled set of COVID-19 cases would not change the median distance to the Huanan market. One can therefore expect that the distance analysis of Worobey et al. would give different results if means were used, but this was not considered in their study.
In the following it is shown, by the authors’ own data, that means, but not medians, introduce the location of the Wuhan Institute of Virology (WIV) as geographically associated with the Huanan market (“the early epicenter of the COVID-19 pandemic”) at the same statistical significance level as the earliest known lineage B cases. Thus the authors’ choice against the use of means resulted in a selective bias against an important alternative hypothesis that is supported by their own data.
Specifically, the mean distance of the n=11 lineage B cases to the Huanan market is 12.2 km (p < 0.025; p-values, with 0.05 significance level, were calculated by direct numerical sampling of the expected distances in their data file “distance_popdensityagegroups_null_1.csv” retrieved from https://github.com/sars-cov-2-origins/huanan-market/tree/main/data). Yet the distance between the Huanan market and the Wuhan Institute of Virology is nearly as far, 12.1 km (the WIV location [30.53930206N, 114.35085239E] corresponds to the institute’s main research and administrative building, see Figure 1A-C; distances measured with both the Google Maps and the Baidu map software tools at 100 m resolution.) This value is equally significant, p < 0.025, when the WIV location is geometrically represented by any tight cluster of n=11 locations in or around the WIV such that their mean distance to the Hunan market is 12.1 km. This outcome is robust: a similar result for n=10 is obtained when the one lineage B case is removed which previously had not been linked epidemiologically with the Huanan market (12.9 km mean distance from Huanan market, p < 0.05). In contrast, when tested against expected n=11 or n=10 medians, the 12.1 km distance is not statistically significant (p < 0.184). Thus an important alternative hypothesis (i.e., WIV is geographically associated with the Huanan market at higher statistical significance than the 11 lineage B cases) is rejected when medians are used, and not rejected when means are tested.
The fact that the mean distance between lineage B cases and the Huanan market is greater or equal than the (mean) distance between the latter and the Wuhan Institute of Virology is relevant because only from this numerical order statistical significance of the former necessitates statistical significance of the latter. In contrast, the 35 cases linked to Huanan market as well as the 120 not epidemiologically linked to it [1] have both statistically significant mean distances (11.7 km and 6.7 km, respectively) that are markedly smaller than 12.1 km; thus for each of these two sets of cases one cannot strictly infer geographical association with the WIV even though the 12.1 km distance is also statistically significant on the n=35 and on the n=120 statistical backgrounds (both p < 0.0001).
In summary, based on the data of Worobey et al., any tight cluster of ten early COVID-19 cases in or around the Wuhan Institute of Virology would be geographically associated with the Huanan market at a higher level of statistical significance than the earliest lineage B cases that already had been linked epidemiologically with the Huanan market. Three main possibilities can then be considered: 1.) Such cluster did not exist in late 2019; 2.) it did exist and was documented but the epidemiological information has not been published yet; 3.) since the WIV is not a residential location the entire cluster or a part of it corresponds to a group of individuals among the 155 cases analysed by Worobey et al. Regarding this third possibility, it is remarkable that the four nearest cases to the WIV form a localized cluster—over roughly one square kilometer at the Shahuxincun neighborhood— with an average distance of 2.7 km to the Wuhan Institute of Virology (Figure 1A).
The critical question if and how many human SARS-CoV-2 infections had actually occurred at the WIV in late 2019 was entirely ignored by Worobey et al. This selective omission is not understandable as reports have existed since at least early 2021 which indicate that it might had been the case. For example, widely circulated official publications by the US government report “with moderate confidence that the first human infection with SARS-CoV-2 most likely was the result of a laboratory-associated incident, probably involving experimentation, animal handling, or sampling by the Wuhan Institute of Virology” [3], and that “[t]he U.S. government has reason to believe that several researchers inside the WIV became sick in autumn 2019, before the first identified case of the outbreak, with symptoms consistent with both COVID-19 and common seasonal illnesses.” [4] Thus the geospatial association of the Wuhan Institute of Virology with the suggested early epicenter of the COVID-19 pandemic, as detected here, might be epidemiologically relevant and therefore deserves further scientific attention.
As no acceptable scientific conclusion to the COVID-19 origins problem should evidently be the product of a selective bias (i.e., the deliberate choice of medians over means with the resulting omission of statistical data associated with the Wuhan Institute of Virology), it is suggested that Worobey et al. change their main interpretations and conclusions accordingly.
Figures
Figure 1A, B, C deposited at Harvard Dataverse (dataverse.harvard.edu):
Lisewski, Andreas Martin, 2022, "Figure 1A-C", https://doi.org/10.7910/DVN/OPRUXQ, Harvard Dataverse, V1
References
[1] Worobey M, Levy JI, Malpica Serrano L, et al. The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic. Science. 2022;377(6609):951-959. doi:10.1126/science.abp8715
[2] Pekar JE, Magee A, Parker E, et al. The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2. Science. 2022;377(6609):960-966. doi:10.1126/science.abp8337
[3] The Office of the Director of National Intelligence (ODNI). Unclassified Summary of Assessment on COVID-19 Origins. 27 August 2021. URL (accessed 7 October 2022): https://www.dni.gov/index.php/newsroom/reports-publications/reports-publications-2021/item/2236-unclassified-summary-of-assessment-on-covid-19-origins
[4] The US Department of State - Office of the Spokesperson. Fact Sheet: Activity at the Wuhan Institute of Virology. 15 January 2021. URL (accessed 7 October 2022): https://2017-2021.state.gov/fact-sheet-activity-at-the-wuhan-institute-of-virology/index.html
Response to "The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic" published on 26 July 2022
eLetter
I read the study of Michael Worobey (1) with interest and appreciation. The authors wrote that environmental samples were taken from vendors’ stalls. Considering the SARS-CoV to be transmitted through respiratory droplets and contact routes, what is the justification for taking the samples from the vendors’ stall only and not from other places in the year 2020 (and in the year 2014 from grates outside vendors’ stall upon which metal cage was stacked)? Another data that the authors used were the social media check-ins in the Sina Visitor System. I do not think that social media check-ins should be considered synonymous with buying some items from the market, and in that case, the proxy of social media check-ins for buying some disease- spreading item from the market is not correct. Lastly, since most of the clustering of early COVID-19 cases occurred near the west bank of Yangtze River, and were detected from the western side of the market where mammal species were sold; I welcome some comments from authors in the light of these epidemiological facts.
References
1. Worobey et al., Science10.1126/science.abp8715 (2022).
Re. this article and the accompanying article
It notable that both this article and the companion article (Pekar JE et al) make no mention of the study published in CID in 2021 in which SARS- CoV-2-reactive antibodies were found in 106 of 7389 serum samples from blood donated to the American Red Cross between mid-December 2019 and mid-January 2020 (1). That study implied the possibility of substantial spread within the US by mid- to late-December, which may seem at odds with the idea that the origin was the Wuhan wet market in late-November to mid-December. Thus, the failure to mention and address that seeming inconsistency may fuel rather than resolve the controversy regarding the origin(s) of the pandemic.
1. Basavaraju SV, et al. Serologic Testing of US Blood Donations to Identify Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)-Reactive Antibodies: December 2019-January 2020. Clin Infect Dis. 2021 Jun 15;72(12):e1004-e1009. doi: 10.1093/cid/ciaa1785. PMID: 33252659; PMCID: PMC7799215.
Proves animals at the market were the source? Falls dreadfully short, giving what's more like a movie treatment.
The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic
gives a description of the start of the pandemic that's been compared to the work of John Snow. Unfortunately, the paper also that led to a global conflagration. Here, the paper falls dreadfully short -- giving what's more like a movie treatment than anything resembling observation, calculation or interpretation.
"They say it was transmitted into people who were working or shopping there in two separate "spillover events", where a human contracted the virus from an animal."
Covid origin studies say evidence points to Wuhan market
https://www.bbc.com/news/science-environment-62307383
The staggeringly sad reality is that reporters won't look at the cites, but will simply accept the authors words as having been proven.
# # #
"The animals on these farms (nearly 1 million) were rapidly released, sold, or killed in early 2020,..."
The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic
"Released back into the woods" ... "Visits to nearly a dozen other former wildlife farms in the area yielded similar stories. Owners were either not home, denied raising animals listed on business registrations, or said they stopped farming before the outbreak."
M. Standaert, E. Dou, “In search for coronavirus origins, Hubei caves and wildlife farms draw new scrutiny,” The Washington Post, 11 October 2021; https://www.washingtonpost.com/world/asia_pacific/china-covid-bats-caves-hubei/2021/10/10/082eb8b6-1c32-11ec-bea8-308ea134594f_story.html.
From the Washington Post article, I can't see where the total of animals on farms is provided. Actually, learning anything about the farms is now an intractable problem for science. Information about the farms is either suppressed or questionable. The WP reporters only state the single answer of "Released back into the woods." Exactly what "similar stories" are is not explained. For the most part, what the WP relays is that information was not available or suspec,
# # #
"There was an extensive network of wildlife farms in western Hubei province, including hundreds of thousands of raccoon dogs on farms in Enshi prefecture, which supplied the Huanan market (48)."
M. Standaert, E. Dou, “In search for coronavirus origins, Hubei caves and wildlife farms draw new scrutiny,” The Washington Post, 11 October 2021; https://www.washingtonpost.com/world/asia_pacific/china-covid-bats-caves-hubei/2021/10/10/082eb8b6-1c32-11ec-bea8-308ea134594f_story.html.
"This region of Hubei contains extensive cave complexes housing Rhinolophus bats, which carry SARSr-CoVs (49). "
X.-D. Lin, W. Wang, Z.-Y. Hao, Z.-X. Wang, W.-P. Guo, X.-Q. Guan, M.-R. Wang, H.-W. Wang, R.-H. Zhou, M.-H. Li, G.-P. Tang, J. Wu, E. C. Holmes, Y.-Z. Zhang, Extensive diversity of coronaviruses in bats from China. Virology507, 1–10 (2017).
In the WP article, Dr. Holmes says that "to his knowledge, bat sampling had been done by scientists near but not inside Enshi, and that no coronaviruses were detected, but he added that the sample sizes were too small.
"I'm certain that SARS-CoV-2-like viruses will be found in China in places where you find Rhinolophus bats," Holmes said."
Certainly coronaviruses in the region's bats is a topic for further investigation -- that's not now politically possible. Still, speculation does not replace observation.
# # #
"Defunct wildlife farms sat as close as one mile from the entrances."
M. Standaert, E. Dou, “In search for coronavirus origins, Hubei caves and wildlife farms draw new scrutiny,” The Washington Post, 11 October 2021; https://www.washingtonpost.com/world/asia_pacific/china-covid-bats-caves-hubei/2021/10/10/082eb8b6-1c32-11ec-bea8-308ea134594f_story.html.
Has it been established how far the Horseshoe bats fly when foraging at night? Has any
means of the bats interacting with the farmed animals been established or speculated? Contaminated fruit is the supposed source of Hendra in Australia and Nipah in other countries. I believe all the suspect bats in China are insectivorous and most of the farmed animals are carnivores. Is there any reason to believe that bats had been collected to be fed to the farmed animals? Are free roaming domestic cats kept on farms in the area for rodent control? If there were infected bats a mile away, as in more standard communication theory, the Last Mile is all important.
On a separate— but related— topic, in China there were no CoViD 19 outbreaks on fur farms as there were in the US, the Netherlands, and Denmark?
# # #
"... a potential source of virus transmission into the human population in late 2019, plausibly from infected live mammals sold at the Huanan market, "
# # #
The China research cited (24) is much more circumspect. They could not link animals or even animal related activity at the market as the source.
"All the four sewerage wells in the market tested positive. This suggested that either contaminated sewage may have played a role in the cluster of cases in the market or that the infected people in the market contaminated the sewage."
"The 457 animal samples mainly collected between January 1st and March 2nd, 2020 included 188 individuals belonging to 18 species (with some stray animals sampled until March 30th) (Table 2). The sources of the samples include unsold goods kept in refrigerators and freezers in the stalls of HSM, and goods kept in warehouses and refrigerators related to the HSM. Samples from stray animals in the market were also collected, i.e. swab samples from 10 stray cats, 27 cat feces, one dog, one weasel, and 10 rats. All the 457 animal samples tested negative for SARS-CoV-2 nucleic acid, suggesting that the animal infections with SARS-CoV-2 might be rare in the market."
Surveillance of SARS-CoV-2 in the environment and animal samples of the Huanan Seafood Market
George Gao et al